Skip to content

Data Portal

The filesystem implementation is a concrete implementation of the abstract copick API that reads data from the cryoET Data Portal and reads/writes data to/from any storage supported by fsspec. The filesystem implementation is defined in the copick.impl.cryoet_data_portal module.

Metadata Models

copick.impl.cryoet_data_portal.CopickConfigCDP

Bases: CopickConfig

Data Entities

copick.impl.cryoet_data_portal.CopickRootCDP

Bases: CopickRoot

copick.impl.cryoet_data_portal.CopickObjectCDP

Bases: CopickObjectOverlay

copick.impl.cryoet_data_portal.CopickRunCDP

Bases: CopickRunOverlay

get_picks 

get_picks(object_name: str = None, user_id: str = None, session_id: str = None, portal_meta_query: Dict[str, Any] = None, portal_author_query: List[str] = None) -> List[CopickPicksCDP]

Get picks by name, user_id or session_id (or combinations). Portal metadata are compared for equality. Portal authors are checked for inclusion in the full author list.

Parameters:

  • object_name (str, default: None ) –

    Name of the object to search for.

  • user_id (str, default: None ) –

    User ID to search for.

  • session_id (str, default: None ) –

    Session ID to search for.

  • portal_meta_query (Dict[str, Any], default: None ) –

    Dictionary of values to compare against portal metadata of this annotation. Allowed keys are the scalar fields of cryoet_data_portal.Annotation

  • portal_author_query (List[str], default: None ) –

    List of author names. Segmentations are included if this author is in the portal annotation's author list.

Returns:

  • List[CopickPicksCDP] –

    List[CopickPicks]: List of picks that match the search criteria.

get_segmentations 

get_segmentations(user_id: str = None, session_id: str = None, is_multilabel: bool = None, name: str = None, voxel_size: float = None, portal_meta_query: Dict[str, Any] = None, portal_author_query: List[str] = None) -> List[CopickSegmentationCDP]

Get segmentations by user_id, session_id, name, type or voxel_size (or combinations) and portal metadata and authors. Portal metadata are compared for equality. Portal authors are checked for inclusion in the full author list.

Parameters:

  • user_id (str, default: None ) –

    User ID to search for.

  • session_id (str, default: None ) –

    Session ID to search for.

  • is_multilabel (bool, default: None ) –

    Whether the segmentation is multilabel or not.

  • name (str, default: None ) –

    Name of the segmentation to search for.

  • voxel_size (float, default: None ) –

    Voxel size to search for.

  • portal_meta_query (Dict[str, Any], default: None ) –

    Dictionary of values to compare against portal metadata of this annotation. Allowed keys are the scalar fields of cryoet_data_portal.Annotation

  • portal_author_query (List[str], default: None ) –

    List of author names. Segmentations are included if this author is in the portal annotation's author list.

Returns:

  • List[CopickSegmentationCDP] –

    List[CopickSegmentation]: List of segmentations that match the search criteria.

ensure 

ensure(create: bool = False) -> bool

Checks if the run record exists in the static or overlay directory, optionally creating it in the overlay filesystem if it does not.

Parameters:

  • create (bool, default: False ) –

    Whether to create the run record if it does not exist.

Returns:

  • bool ( bool ) –

    True if the run record exists, False otherwise.

copick.impl.cryoet_data_portal.CopickPicksCDP

Bases: CopickPicksOverlay

copick.impl.cryoet_data_portal.CopickMeshCDP

Bases: CopickMeshOverlay

copick.impl.cryoet_data_portal.CopickSegmentationCDP

Bases: CopickSegmentationOverlay

copick.impl.cryoet_data_portal.CopickVoxelSpacingCDP

Bases: CopickVoxelSpacingOverlay

ensure 

ensure(create: bool = False) -> bool

Checks if the voxel spacing record exists in the static or overlay directory, optionally creating it in the overlay filesystem if it does not.

Parameters:

  • create (bool, default: False ) –

    Whether to create the voxel spacing record if it does not exist.

Returns:

  • bool ( bool ) –

    True if the voxel spacing record exists, False otherwise.

get_tomograms 

get_tomograms(tomo_type: str, portal_meta_query: Dict[str, Any] = None, portal_author_query: List[str] = None) -> List[CopickTomogramCDP]

Get a tomogram by type. Portal metadata are compared for equality. Authors are compared for inclusion.

Parameters:

  • tomo_type (str) –

    The type of tomogram to get. For portal tomograms, this is cryoet_data_portal.Tomogram.reconstruction_method.

  • portal_meta_query (Dict[str, Any], default: None ) –

    Dictionary of values to compare against portal metadata of this tomogram. Allowed keys are the scalar fields of cryoet_data_portal.Tomogram

  • portal_author_query (List[str], default: None ) –

    List of author names. Tomograms are included if this author is in the portal annotation's author list.

Returns:

  • List[CopickTomogramCDP] –

    List[CopickTomogram]: The list of tomograms that match the query.

copick.impl.cryoet_data_portal.CopickTomogramCDP

Bases: CopickTomogramOverlay

tomo_type 

tomo_type: str

The type of tomogram. For data portal tomograms, this is derived as cryoet_data_portal.Tomogram.reconstruction_method + "-" + cryoet_data_portal.Tomogram.processing + ["-" + cryoet_data_portal.Tomogram.processing_software + "-" + cryoet_data_portal.Tomogram.ctf_corrected], where cryoet_data_portal.Tomogram.processing_software and cryoet_data_portal.Tomogram.ctf_corrected are discarded if null in the database.

portal_tomo 

portal_tomo: bool

Whether this tomogram is from the portal or not.

copick.impl.cryoet_data_portal.CopickFeaturesCDP

Bases: CopickFeaturesOverlay